You don't say what size frame you got. I'm 5'4 1/2" and my last Trek was a 16" frame, I remember. This was with 700c wheels. You need to consider wheels size, frame size, and also how the downtube runs (is it straight or angled down, is the bike a step through model). Sizing a bike just based on wheels size is not a great idea. Since you enjoyed riding the 26" wheel bike, maybe that frame size was a good fit, but you might do better with a 24" wheel on that frame size. Were the bikes both the same frame size?
Also, your height is less important than your inseam. Mine is 29.5" for that 16" frame. If the shop you purchased at can't properly fit you to frame size + wheel size, go somewhere else.
And, you are tilting the bike when you stop, right? You don't just stop with the bike perfectly vertical. You lean the bike which allows you to get that foot down flat.